org.rcsb.openmms.meta
Class FieldTrans

java.lang.Object
  |
  +--org.rcsb.openmms.meta.Trans
        |
        +--org.rcsb.openmms.meta.FieldTrans

Direct Known Subclasses:

MatrixTrans, SubfieldTrans, VectorTrans

public class FieldTrans

extends Trans

Class for "Fields" in Cif Metamodel

Version:

1.6

Author:

Douglas S. Greer

Field Summary

protected java.lang.String	columnIndexName
protected java.lang.String	columnName names for building sql tables
protected java.lang.String	copyName Name of "extra" copy used in constructing symetric matrices
int	descriptionParagraphs
protected java.lang.String	fieldType Non-Cif fields must explictly declare their type
protected java.lang.String	fullFieldName prefixed with list of embedded field structure names using "."
protected java.lang.String	fullRefName prefixed with list of embedded field structure names using "_"
static int	IS_A_STREAM_DATATYPE
protected boolean	isCifField
protected boolean	pseudoField Indicates fields used to roll-up vectors and matrices in mmCIF into the correct Vectore and Matrix3 structures
protected java.lang.String	realName "real" name used to generate vector/matrix code that correctly indexes values with "n" instead of "n+1"
protected StructureTrans	structType Pointer to the structure node when a structure type used as a field element.

Constructor Summary

FieldTrans(java.lang.String n)

FieldTrans(java.lang.String varname, java.lang.String cifname)

FieldTrans(java.lang.String rtype, java.lang.String varname, boolean icf)

FieldTrans(java.lang.String varname, java.lang.String cifname, int descp)

FieldTrans(StructureTrans st, java.lang.String varname)
Constructor used for embedded structs

Method Summary

void	accept(TransVisitor v)
java.lang.String	cifNameToTagName(java.lang.String cname) Converts the left brackets and periods to underbars and deletes the right brackets
protected java.lang.String	computeFullName(char c) Overridded by SubfieldTrans and MatrixTrans For Fields and Subfields this will return the name of a basic type only if getFieldStructure() returns null.
void	computeNames()
java.lang.String	getCifItemName() This method must return a valid mmCIF dictionary reference
FieldTrans	getCifParentIndex()
java.lang.String	getColumnIndexName()
java.lang.String	getColumnName()
FieldTrans	getContainingField()
java.lang.String	getCopyName()
DictionaryItem	getDictionaryItem()
StructureTrans	getFieldStructure() for fields that are of type struct, returns a pointer to the struct declaration; otherwise returns null
java.lang.String	getFieldType() returns a string representing the type of this field type
java.lang.String	getFieldType(ModuleTrans inMod) returns a string representing the type of this field If the type is a structure name, then the fully qualified name will be returned if the structure is not in the current module as specified by inMod.
java.lang.String	getFlagName()
java.lang.String	getFullFieldName()
java.lang.String	getFullRefName()
java.lang.String	getRealName()
StructureTrans	getStructure()
java.lang.String	getTagName()
boolean	isCifField()
boolean	isFieldBitSet(int f)
boolean	isIndexField()
boolean	isLeaf() A leaf field node is anything that does not have a structure type, and therefore never has children.
boolean	isPseudoField() Pseudo Fields represent the individual elements in an array (e.g. the unrolled mmCIF vectors/matrices)
void	setCifParentIndex(FieldTrans p)
void	setColumnIndexName(java.lang.String s)
void	setColumnName(java.lang.String s)
void	setCopyName(java.lang.String s)
void	setDictionaryItem(DictionaryItem di)
void	setFieldBit(int f)
void	setFieldStructure(StructureTrans st)
void	setPseudoField(boolean pf) Pseudo Fields represent the individual elements in an array (e.g. the unrolled mmCIF vectors/matrices)
void	setRealName(java.lang.String s)
void	setStructure(StructureTrans st)

Methods inherited from class org.rcsb.openmms.meta.Trans

add, convertToFlagName, convertToUnderbar, getBlankLines, getChild, getComment, getName, getTransType, numberOfChildren, replace, setBlankLines, setComment, setTransType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

realName

protected java.lang.String realName

"real" name used to generate vector/matrix code that correctly indexes values with "n" instead of "n+1"

fullFieldName

protected java.lang.String fullFieldName

prefixed with list of embedded field structure names using "."

fullRefName

protected java.lang.String fullRefName

prefixed with list of embedded field structure names using "_"

copyName

protected java.lang.String copyName

Name of "extra" copy used in constructing symetric matrices

columnName

protected java.lang.String columnName

names for building sql tables

columnIndexName

protected java.lang.String columnIndexName

isCifField

protected boolean isCifField

fieldType

protected java.lang.String fieldType

Non-Cif fields must explictly declare their type

structType

protected StructureTrans structType

Pointer to the structure node when a structure type used as a field element.

pseudoField

protected boolean pseudoField

Indicates fields used to roll-up vectors and matrices in mmCIF into the correct Vectore and Matrix3 structures

IS_A_STREAM_DATATYPE

public static final int IS_A_STREAM_DATATYPE

See Also:

Constant Field Values

descriptionParagraphs

public int descriptionParagraphs

Constructor Detail

FieldTrans

public FieldTrans(java.lang.String n)

FieldTrans

public FieldTrans(java.lang.String varname,
                  java.lang.String cifname)

FieldTrans

public FieldTrans(java.lang.String rtype,
                  java.lang.String varname,
                  boolean icf)

FieldTrans

public FieldTrans(StructureTrans st,
                  java.lang.String varname)

Constructor used for embedded structs

FieldTrans

public FieldTrans(java.lang.String varname,
                  java.lang.String cifname,
                  int descp)

Method Detail

accept

public void accept(TransVisitor v)
            throws java.io.IOException,
                   TransGenException

Specified by:

accept in class Trans

java.io.IOException

TransGenException

setStructure

public void setStructure(StructureTrans st)

getStructure

public StructureTrans getStructure()

setDictionaryItem

public void setDictionaryItem(DictionaryItem di)

getDictionaryItem

public DictionaryItem getDictionaryItem()

getCifItemName

public java.lang.String getCifItemName()

This method must return a valid mmCIF dictionary reference

setPseudoField

public void setPseudoField(boolean pf)

Pseudo Fields represent the individual elements in an array (e.g. the unrolled mmCIF vectors/matrices)

isPseudoField

public boolean isPseudoField()

Pseudo Fields represent the individual elements in an array (e.g. the unrolled mmCIF vectors/matrices)

isCifField

public boolean isCifField()

computeNames

public void computeNames()

computeFullName

protected java.lang.String computeFullName(char c)

Overridded by SubfieldTrans and MatrixTrans For Fields and Subfields this will return the name of a basic type only if getFieldStructure() returns null. Otherwise it has type getFieldStructure().getName() Note that private methods are not overriden, so this method must declared with at least protected access.

getFullFieldName

public java.lang.String getFullFieldName()

getFullRefName

public java.lang.String getFullRefName()

isLeaf

public boolean isLeaf()

A leaf field node is anything that does not have a structure type, and therefore never has children.

setFieldStructure

public void setFieldStructure(StructureTrans st)

getFieldStructure

public StructureTrans getFieldStructure()

for fields that are of type struct, returns a pointer to the struct declaration; otherwise returns null

getFieldType

public java.lang.String getFieldType()

returns a string representing the type of this field type

getFieldType

public java.lang.String getFieldType(ModuleTrans inMod)

returns a string representing the type of this field If the type is a structure name, then the fully qualified name will be returned if the structure is not in the current module as specified by inMod.

getFlagName

public java.lang.String getFlagName()

getTagName

public java.lang.String getTagName()

setRealName

public void setRealName(java.lang.String s)

getRealName

public java.lang.String getRealName()

setCopyName

public void setCopyName(java.lang.String s)

getCopyName

public java.lang.String getCopyName()

setColumnName

public void setColumnName(java.lang.String s)

getColumnName

public java.lang.String getColumnName()

setColumnIndexName

public void setColumnIndexName(java.lang.String s)

getColumnIndexName

public java.lang.String getColumnIndexName()

getContainingField

public FieldTrans getContainingField()

setCifParentIndex

public void setCifParentIndex(FieldTrans p)

isIndexField

public boolean isIndexField()

getCifParentIndex

public FieldTrans getCifParentIndex()

setFieldBit

public void setFieldBit(int f)

isFieldBitSet

public boolean isFieldBitSet(int f)

cifNameToTagName

public java.lang.String cifNameToTagName(java.lang.String cname)

Converts the left brackets and periods to underbars and deletes the right brackets